Contributors FS, GR, CvdG, PM, LV, MC, LH, TD, NP, BF and KB were all involved in the conception, design, interpretation of data, and
revising and final approval of the article. In addition, CvdG and LV were responsible for statistical analysis, and TD for
sample and metadata collection. GR is the guarantor. In addition, collaborator KD was involved in the processing of samples,
PC in data processing.

Received 10 August 2011

Accepted 9 May 2012

Published Online First 15 June 2012

Abstract

Background Culture-independent analysis of the respiratory secretions of people with cystic fibrosis (CF) has identified many bacterial
species not previously detected using culture in this context. However, little is known about their clinical significance
or persistence in CF airways.

Methods The authors characterised the viable bacterial communities in the sputum collected from 14 patients at monthly intervals
over 1 year using a molecular community profiling technique—terminal restriction fragment length polymorphism. Clinical characteristics
were also collected, including lung function and medications. Ecological community measures were determined for each sample.
Microbial community change over time within subjects was defined using ecological analytical tools, and these measures were
compared between subjects and to clinical features.

Results Bacterial communities were stable within subjects over time but varied between subjects, despite similarities in clinical
course. Antibiotic therapy temporarily perturbed these communities which generally returned to pretreatment configurations
within 1 month. Species usually considered CF pathogens and those not previously regarded as such exhibited similar patterns
of persistence. Less diverse sputum bacterial communities were correlated to lung disease severity and relative abundance
of Pseudomonas aeruginosa.

Conclusion Whilst not true in all cases, the microbial communities that chronically infect the airways of patients with CF can vary
little over a year despite antibiotic perturbation. The species present tended to vary more between than within subjects,
suggesting that each CF airway infection is unique, with relatively stable and resilient bacterial communities. The inverse
relationship between community richness and disease severity is similar to findings reported in other mucosal infections.

Footnotes

Linked article YES

Funding This work was supported by the Anna Trust (grant number KB2008) and the Seattle Children's Hospital Center for Clinical and
Translational Research.

Competing interests None.

Patient consent Detail has been removed from this case description/these case descriptions to ensure anonymity. The editors and reviewers
have seen the detailed information available and are satisfied that the information backs up the case the authors are making.

Ethics approval Ethics approval was provided by Southampton and South West Hampshire Research Ethics Committee.